Can't Insert Special Characters WYSIWYG with CKEDITOR

The reason we do this is that content in non-English or non-Latin languages would otherwise contain plenty of converted HTML entities and potentially not a single plain character anymore. I.e., someone writing a post in Greek would see total garbage when looking at the HTML source code.

It looks like you tried to override the configuration via JS - however, did you already try to override it via the settings alter hook?

The reason modifying config.js didn't work is because it's not being loaded. Wysiwyg generates all settings for the editor and passes them directly to the new editor instance when it's created.

As Sun said, you can override the generated settings, or add new ones, by implementing hook_wysiwyg_editor_settings_alter() in a custom module. (Example in wysiwyg.api.php and the issue queue.)

It should look something like this: (I can't guarantee these are the values you're looking for, just translating the snippet you posted to PHP for use in the hook.)

function MYMODULE_wysiwyg_editor_settings_alter(&$settings, $context) {
 if ($context['profile']->editor == 'ckeditor') {
   $settings['htmlEncodeOutput'] = FALSE;
   $settings['entities'] = FALSE;
 }
}

I don't think this is a bug but more of a consequence of the settings Drupal/Wysiwyg use as defaults.

Please use <code></code> tags when posting snippets and special characters, makes it easer to determine if you really mean the literal Δ or the entity Δ.
Am I right in that you want to store Δ as a single character, but get Δ instead?
Setting the "entites", "entities_latin", "entities_greek" options to FALSE should stop the editor from inserting new glyphs as &something; entities, and prevent it from converting existing glyphs to entites as well. Wysiwyg sets the latter two to FALSE by default, and you set the first one to FALSE as well, so it should work. I made some quick tests with Wysiwyg's default settings and it showed up as Δ, at least when copy/pasting from here. Inserting Δ into the source also got converted to Δ.

Are you using a math filter for rendering this content? The error suggests something is going wrong on the server after the content has been submitted. Wysiwyg doesn't run any code a that point, it just detaches the editor before the form is submitted (same thing that happens if you click "Disable rich-text") to make the contents sync back to the original textarea.
Do you see any more detailed errors in any Drupal/PHP logs?

Btw, if you're using the Teaser Break plugin, please disable it and test without it, just to rule it out.

This is a completely unacceptable situation. HTML special characters need to be encoded, and every time I try to change quotation marks using either entities or their unicode equivalents, these are being turned back to normal text. This has the possibility of causing browser errors. I shouldn't have to create a new module to rectify this situation. At present, I'm going to look for a different module.

Thanks for the clarification, I first thought you wanted the opposite result.

I don't understand what browser errors you're talking about, all browsers I'm aware of handle Unicode/UTF-8 fine, which is what Drupal outputs. W3's validator does not complain when not using Δ either. This is why Wysiwyg changes CKEditor's entities_greek setting to false. See http://htmlpurifier.org/docs/enduser-utf8.html#whyutf8 for a quick explanation.

I've not encountered any serverside errors when submitting non-entity Delta characters either, do any of the logs (Drupal, server etc) show any more details about the errors? You might need to change which PHP errors are displayed on the screen, since what you saw is a generic error displayed when the page could not be generated due to a fatal error. Sounds a lot like a module got can't handle Unicode/UTF-8 content. That might cause subtle errors elsewhere so I'd investigate that further by either testing with a fresh installation and adding modules until the errors happen, or by disabling modules on the site until the error goes away, to find out where things go wrong.

Anyway, I have confirmed that you can override Wysiwyg's settings for CKEditor like this

function MYMODULE_wysiwyg_editor_settings_alter(&$settings, $context) {
 if ($context['profile']->editor == 'ckeditor') {
   $settings['entities_greek'] = TRUE;
   $settings['entities_additional'] = 'quot';
 }
}

and it will output the Delta character as Δ and change the Quote character as well. It's very common to have a customization module for each site and this snippet could go there. In the future we'll create a GUI to change settings like this, at which point the snippet won't be needed anymore.

I have also confirmed that the Teaser Break plugin will convert Δ back to Δ, so it needs to stay disabled until we can fix that.

This has the possibility of causing browser errors.

As @TwoD already explained, this statement is invalid.

I don't think there's anything we can reasonably do here, as we're already doing the best that can be done to make HTML characters/entities conversion not break on multilingual or in general non-English sites. Also, I don't want to see a setting for this in the future.